rbbt-sources 3.0.2 → 3.0.3
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/biomart.rb +1 -1
- data/lib/rbbt/sources/kegg.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
|
3
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+
metadata.gz: a5f75097d1a73830c5ae3c2749b114d50367862e
|
4
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+
data.tar.gz: 837d1281d60d46d97690eaefb36dcfa1e5636636
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5
5
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SHA512:
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6
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-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
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+
metadata.gz: 38695de62c02838192de10b51b2be02ab6800aa2a62aa96843049325fe6360140433f348d974f18059967f45b76edc621079f9a59d0d521dca491a5ac8182689
|
7
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+
data.tar.gz: 7223c40d440690cb5ccab506a580593d3adec269060b3006caf8b2985d68b2b564ac0a6eaf3d5f476cb2e6ae483c940525f20fc2df8be28dae03283cb64fe7f1
|
data/lib/rbbt/sources/biomart.rb
CHANGED
@@ -167,7 +167,7 @@ module BioMart
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167
167
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data = get(database, main, [], filters, data, open_options)
|
168
168
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end
|
169
169
|
|
170
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-
open_options[:filename]
|
170
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+
open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
|
171
171
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if filename.nil?
|
172
172
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results = TSV.open data, open_options
|
173
173
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results.key_field = main
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data/lib/rbbt/sources/kegg.rb
CHANGED
@@ -110,11 +110,11 @@ if defined? Entity
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|
110
110
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self
|
111
111
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when format == "KEGG Gene ID"
|
112
112
|
ensembl = from_kegg.clean_annotations
|
113
|
-
Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).
|
113
|
+
Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).run.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
|
114
114
|
when new_format == "KEGG Gene ID"
|
115
115
|
to_kegg
|
116
116
|
else
|
117
|
-
Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).
|
117
|
+
Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).run.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
|
118
118
|
end
|
119
119
|
end
|
120
120
|
|
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-sources
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 3.0.
|
4
|
+
version: 3.0.3
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2014-
|
11
|
+
date: 2014-04-14 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rbbt-util
|